Saving 3D image

Hi,

I have a series of CT image slices that I've uploaded into MATLAB and are stacked in one variable. How do I save it out as a 3D image?

Answer 1

[Sean de Wolski]

Does it need to be accessible from another program?

doc save

I would just use save and save it as a matfile. If it has to be readable from another program (or someone without MATLAB) use fopen/fwrite

doc fopen
doc fwrite

[Ka Zhang]

Yes, I'm using another program called elastix for image registration. It's ran from a command line, so I don't think fopen/fwrite will work. Thanks!

[Sean de Wolski]

fopen/fwrite will write it to binary. What format does elastix require? You're going to have to write to that format if elastix doesn't except raw binary.

[Ka Zhang]

For elastix TIFF, JPEG, PNG, BMP, and DICOM seem to be common. Is there any way I could save my variable with all the slices as one of those formats?

[Walter Roberson]

DICOM could do that for sure, in a format that elastix would be likely to understand.

The TIFF format does allow multiple images per file, but you would have to know exactly how elastix wanted the images named (or numbered)... and considering that JPEG and PNG and BMP files cannot handle multiple images per file, I would think it likely that elastix is not designed to look for the possibility of all of the slices being stored in the one TIFF file.

[Ka Zhang]

Is there anything special I need to specify with dicomwrite for a 3D variable? I'm getting errors when using dicomwrite.

[Sean de Wolski]

How are you calling dicomwrite and what are the _full_ error messages?

[Ka Zhang]

>> dicomwrite('images','027_3D.dcm');

??? Error using ==> dicom_prep_ImagePixel>getPixelStorage at 168

Invalid datatype for image pixels.

Error in ==> dicom_prep_ImagePixel at 14

[ba, bs, hb, pr] = getPixelStorage(X, txfr);

Error in ==> dicom_prep_metadata at 40

metadata = dicom_prep_ImagePixel(metadata, X, map, txfr);

Error in ==> dicom_create_IOD at 30

metadata = dicom_prep_metadata(IOD_UID, metadata, X, map, options.txfr);

Error in ==> dicomwrite>write_message at 236

[attrs, msg, status] = dicom_create_IOD(SOP_UID, X(:,:,:,p), map, ...

Error in ==> dicomwrite at 195

status = write_message(X, filename, map, metadata, options);

[Sean de Wolski]

You're calling dicomwrite with 'images' which is a 1x6 string (typo, probably).

dicomwrite(images,'027_3D.dcm');

[Ka Zhang]

oops that was silly. But it seems it is not the problem:

>> dicomwrite(image027,'027_3D.dcm');

??? Error using ==> dicom_prep_ImagePixel>getPhotometricInterp at 98

Cannot determine photometric interpretation.

Error in ==> dicom_prep_ImagePixel at 10

metadata.(dicom_name_lookup('0028', '0004')) = getPhotometricInterp(X, map, txfr);

Error in ==> dicom_prep_metadata at 40

metadata = dicom_prep_ImagePixel(metadata, X, map, txfr);

Error in ==> dicom_create_IOD at 30

metadata = dicom_prep_metadata(IOD_UID, metadata, X, map, options.txfr);

Error in ==> dicomwrite>write_message at 236

[attrs, msg, status] = dicom_create_IOD(SOP_UID, X(:,:,:,p), map, ...

Error in ==> dicomwrite at 195

status = write_message(X, filename, map, metadata, options);

[Sean de Wolski]

what does

whos images

return?

[Ka Zhang]

it's

Name Size Bytes Class Attributes

image027 512x512x99 207618048 double

Answer 2

[Walter Roberson]

http://www.mathworks.com/matlabcentral/answers/343-dicomwrite-function-help-needed

[Ka Zhang]

unfortunately that writes out the 3D MATLAB variable into 2D slices with each slice as an individual dicom file. Thanks though